Dataset Information

OpenGenomeBrowser: a versatile, dataset-independent and scalable web platform for genome data management and comparative genomics.

ABSTRACT:

Background

As the amount of genomic data continues to grow, there is an increasing need for systematic ways to organize, explore, compare, analyze and share this data. Despite this, there is a lack of suitable platforms to meet this need.

Results

OpenGenomeBrowser is a self-hostable, open-source platform to manage access to genomic data and drastically simplifying comparative genomics analyses. It enables users to interactively generate phylogenetic trees, compare gene loci, browse biochemical pathways, perform gene trait matching, create dot plots, execute BLAST searches, and access the data. It features a flexible user management system, and its modular folder structure enables the organization of genomic data and metadata, and to automate analyses. We tested OpenGenomeBrowser with bacterial, archaeal and yeast genomes. We provide a docker container to make installation and hosting simple. The source code, documentation, tutorials for OpenGenomeBrowser are available at opengenomebrowser.github.io and a demo server is freely accessible at opengenomebrowser.bioinformatics.unibe.ch .

Conclusions

To our knowledge, OpenGenomeBrowser is the first self-hostable, database-independent comparative genome browser. It drastically simplifies commonly used bioinformatics workflows and enables convenient as well as fast data exploration.

SUBMITTER: Roder T

PROVIDER: S-EPMC9795662 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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Publications

OpenGenomeBrowser: a versatile, dataset-independent and scalable web platform for genome data management and comparative genomics.

Roder Thomas T Oberhänsli Simone S Shani Noam N Bruggmann Rémy R

BMC genomics 20221227 1

<h4>Background</h4>As the amount of genomic data continues to grow, there is an increasing need for systematic ways to organize, explore, compare, analyze and share this data. Despite this, there is a lack of suitable platforms to meet this need.<h4>Results</h4>OpenGenomeBrowser is a self-hostable, open-source platform to manage access to genomic data and drastically simplifying comparative genomics analyses. It enables users to interactively generate phylogenetic trees, compare gene loci, brows ...[more]

PMID: 36575383

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Project description:BackgroundThe Food and Drug Administration Center for Biologics Evaluation and Research (CBER) established the Biologics Effectiveness and Safety (BEST) Initiative with several objectives, including the expansion and enhancement of CBER's access to fit-for-purpose data sources, analytics, tools, and infrastructures to improve the understanding of patient experiences with conditions related to CBER-regulated products. Owing to existing challenges in data collection, especially for rare disease research, CBER recognized the need for a comprehensive platform where study coordinators can engage with study participants and design and deploy studies while patients or caregivers could enroll, consent, and securely participate as well.ObjectiveThis study aimed to increase awareness and describe the design, development, and novelty of the Survey of Health and Patient Experience (SHAPE) platform, its functionality and application, quality improvement efforts, open-source availability, and plans for enhancement.MethodsSHAPE is hosted in a Google Cloud environment and comprises 3 parts: the administrator application, participant app, and application programming interface. The administrator can build a study comprising a set of questionnaires and self-report entries through the app. Once the study is deployed, the participant can access the app, consent to the study, and complete its components. To build SHAPE to be scalable and flexible, we leveraged the open-source software development kit, Ionic Framework. This enabled the building and deploying of apps across platforms, including iOS, Android, and progressive web applications, from a single codebase by using standardized web technologies. SHAPE has been integrated with a leading Health Level 7 (HL7®) Fast Healthcare Interoperability Resources (FHIR®) application programming interface platform, 1upHealth, which allows participants to consent to 1-time data pull of their electronic health records. We used an agile-based process that engaged multiple stakeholders in SHAPE's design and development.ResultsSHAPE allows study coordinators to plan, develop, and deploy questionnaires to obtain important end points directly from patients or caregivers. Electronic health record integration enables access to patient health records, which can validate and enhance the accuracy of data-capture methods. The administrator can then download the study data into HL7® FHIR®-formatted JSON files. In this paper, we illustrate how study coordinators can use SHAPE to design patient-centered studies. We demonstrate its broad applicability through a hypothetical type 1 diabetes cohort study and an ongoing pilot study on metachromatic leukodystrophy to implement best practices for designing a regulatory-grade natural history study for rare diseases.ConclusionsSHAPE is an intuitive and comprehensive data-collection tool for a variety of clinical studies. Further customization of this versatile and scalable platform allows for multiple use cases. SHAPE can capture patient perspectives and clinical data, thereby providing regulators, clinicians, researchers, and patient advocacy organizations with data to inform drug development and improve patient outcomes.

Dataset Information

OpenGenomeBrowser: a versatile, dataset-independent and scalable web platform for genome data management and comparative genomics.

Background

Results

Conclusions

Publications

OpenGenomeBrowser: a versatile, dataset-independent and scalable web platform for genome data management and comparative genomics.

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